spkTools (version 1.28.0)

spkGNN: Genes Needed to Detect N True Positives

Description

Computes the number of genes one would need to consider to obtain a given number of truly positive genes if one considered genes in order of decreasing observed fold change.

Usage

spkGNN(n, n.expr, n.unexpr, AccuracySlope, AccuracySD, nullfc)

Arguments

n

the desired number of true positives

n.expr

the actual number of truly expressed genes

n.unexpr

the actual number of truly unexpressed genes

AccuracySlope

the signal detect slope from the spkSlope function

AccuracySD

the standard deviation of the signal detect slope from the spkAccSD function

nullfc

a vector of null fold changes from the spkBox function

Value

This function returns the expected number of genes one would have to consider to obtain N true positives under the given conditions.

Examples

data(affy)
spkSlopeOut <- spkSlope(affy)
spkBoxOut <- spkBox(affy, spkSlopeOut, fc=2)
AccuracySlope <- round(spkSlopeOut$slope[-1], digits=2)
AccuracySD <- round(spkAccSD(affy, spkSlopeOut), digits=2)
spkGNN(n=25, n.expr=100, n.unexpr=10000, AccuracySlope[2],
AccuracySD[2], spkBoxOut[[2]])